[gmx-developers] itp file format for OPLS force field in Gromacs
feenstra at chem.vu.nl
Mon Mar 24 09:29:56 CET 2003
Ranjit Sudhakar Ranbhor wrote:
> I want to do MD of a nonheme iron enzyme (enzyme substrate complex;
> 1KW9.pdb) using Gromacs. But I guess there are no C6 and C12 parameters
> defined for naked iron (Fe). Therefore I switched over to OPLS force
> field (in which there are c6 and c12 parameters defined for Fe). I have
> sustrate's itp file (downloaded from PRODRG server) for gromacs force
> field. I want to convert it into the format required for OPLS. Kindly
> find an attached substrate itp file (gromacs format).
> Please give necessary guidelines.
You will have to change all 'gromacs' atom types to the corresponding
'OPLS' atom types. IIRC, bonds, angles and dihedrals in OPLS are derived
from the atom type combinations, so those will change 'automagically'.
You will have to use your own knowledge of the substrate molecule and/
or your chemical intuition to decide which are the appropriate OPLS atom
types to use.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |
More information about the gromacs.org_gmx-developers